Abstract
Admixture is an evolutionary process that enables short-term adaptation.
The Creole cattle from Guadeloupe is a tropically adapted breed. Its
three-way admixture and long-term isolation offer a unique opportunity
for understanding the genetic determinants of adaptive admixture in
livestock. Here, we sequenced 23 Creole cattle from Guadeloupe (GUA) and
combined our data with sequenced genomes of 99 cattle from 25 breeds
representative of European, African and indicine groups to provide the
most detailed exploration, to date, of patterns of genetic variation and
to detect selection signatures in this population. We detect 17 228 983
single nucleotide polymorphisms (SNPs) and we confirmed the higher level
of African and indicine ancestries, compared to the European ancestry,
in the GUA genome. We show that, unlike Criollo cattle, GUA population
originates directly from West Africa with indicine ancestry inherited
via West African ancestors. We relied on consistency of signals across
various methods based on excess of haplotype homozygosity, differences
in allele frequencies and excess ⁄ deficiency of local ancestry to
identify five strong candidate regions showing an excess of indicine
ancestry. These encompass immune-, heat-tolerance- and physical
exercise-related genes. Moreover, we found that a previously identified
horn-related gene, RXFP2 is under strong selective pressure in GUA
genome likely owing to human-driven (socio-cultural) pressure. Our study
highlights the role played by population admixture for driving rapid
adaptive response to local environmental constraints.